Yes, in most cases those charges do come through with the room rate, although how clearly they are described depends on the supplier behind that particular rate. Where a property collects a mandatory resort fee, a local tourist or city tax, or a cleaning charge at check in rather than at the time of booking, that information normally arrives alongside the price as a separate note. It will usually say what the charge is for and whether it applies per room per night or per person per stay, so you can see it before you confirm anything.
Because it comes through with the rate, you can show it on your own quote and repeat it on the voucher you send your customer, so there is no surprise when they arrive. Many agents make a habit of reading that part out to the customer on the phone, since a tax collected locally is the single most common reason a traveller rings back feeling they were overcharged.
Be aware of the limits. Some suppliers give these charges as plain wording rather than as a tidy separate amount, so it is not always something you can add up automatically. Local taxes also change from time to time at the destination, and a hotel can occasionally collect something that was not declared when the rate was loaded. We pass on what the supplier sends us and cannot guarantee it is complete for every property in every country.
Before you confirm a room, read the rate notes that come back with it, and for a destination you do not know well it is worth asking the supplier or the hotel directly what is payable on arrival.